If you've got the deck off, I would be tempted to use wood packing (either Marine or hardwood - encapsulated in Epoxy, a perfect job for the off cuts box ) and predrill (hole cutter) well oversize and fill with epoxy when in situ.....the idea being to cope with compression, plus being oversize means don't have to get too precise on the drilling through (to a backing pad).

Each little square of coring should have had resin surround it, or at least, most of it. Which was done in my case. The water only progresses a short distance and stopped.

In these pictures below you can see the resin between the squares. This was a padeye that had been moved w/o proper pre-drill/coring procedures. Fortunately, it only progressed about 2" around the padeye. The PO just kept tightening the studs until it became a hallow in the deck and interior.

At least with sectional coring systems, they are EZ to dry out by drilling holes on the inside and running a fan. With a plywoodcore it would take a long time to dry out. A solid FRP deck would be costly and heavy.

Every construction method has it's +'s and -'s!!!!!! Prevention is the key.

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__________________Faithful are the Wounds of a Friend, but the Kisses of the Enemy are Deceitful! ........
A nation of sheep breeds a government of wolves!
Unprepared boaters, end up as floatsum!.......

Hope the OP is going to use something other than Balsa to re-core his deck. I like 5lb. ridgid urethane for deck coring. Stuff that can't rot is good for a boat. I've done at least a hundred deck corereplacements this way and have yet to do any warranty work on foam core. Balsa is just silly for boats IMHO....

Thanks for all the intelligent replies. I will definitely be looking into an alternate material to replace the balsa. Interestingly, the deck was cored with a strip of ply running (athwartships?) above the transom and another under the mizzen plate. All the rest was balsa blocks. The water can clearly be seen running along the channels between the blocks which has resulted in the rot spreading a lot further than if the gaps had been filled, thanks again folks,
fair winds and clear skies, SoulJah

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A wise man learns by listening,
an average man learns by his experience,
a fool doesn't learn, he knows everything already

When I bought my C&C Redwing in'84, there had been considerable ingress of water into the balsa cabin top, around the handrail mounts.
I determined where the inner and outer skins met, just above the portlights, and drilled a series of 3/8" holes in a horizontal line.
Split a piece of thin wall butyl pipe, and duct taped into over the holes. sealed ends, and connected it to a timer on my shop vac.
Did the same pipe thing over the handrail holes, but with a small forced air heater.
The styrene extracted was foul stuff, but the repair, like Delmarrey did, is still good.

Oh!! afterthought. If you plan on using this method to infuse resin, remember the vapors are explosive. Any vacuum system should be suitably engineered forflammable atmospheres.

We do this instead of "double drilling". It's a much better technique. If you double drill you've removed the skin around the hole and are now relying on the epoxy's bond to the core, with no protection for the brittle epoxy from compression. Just drill the hole exactly the size you need and then remove the core for about 1/2" depth all around the hole. Fill with thickened epoxy to reattach the skins to each other and seal the core. I often use a router bit chucked into a cordless drill to remove the core, does a perfect job in seconds with no core remnant stuck to the skins. Thicken with cabosil for this, you wont be sanding it and you want it strong.

+1
I really like the sound of this technique. Seems to me that the structural integrity is maintained the best.

__________________One must live the way one thinks, or end up thinking the way one lives - Paul Bourget

We do this instead of "double drilling". It's a much better technique. If you double drill you've removed the skin around the hole and are now relying on the epoxy's bond to the core, with no protection for the brittle epoxy from compression. Just drill the hole exactly the size you need and then remove the core for about 1/2" depth all around the hole. Fill with thickened epoxy to reattach the skins to each other and seal the core. I often use a router bit chucked into a cordless drill to remove the core, does a perfect job in seconds with no core remnant stuck to the skins. Thicken with cabosil for this, you wont be sanding it and you want it strong.

Ok, I'll bite. I'm trying to understand this technique. You drill a 1/4 hole through the glass, core and glass, then you use a router bit to open up the core to half an inch around the hole, Yes?

What sort of router bit are you using? I'd like to see a picture as I can't think of a balanced bit that will fit through a 1/4 inch hole yet allow you to carve away coring half an inch away from the sides of the hole.

Only for holes about 3/4" and up. Obviously this doesn't work for a hole as small as 1/4", nor would most other methods of core removal. Most people would just use a proper bedding compound for a hole that small, but if you are worried about core compression or are for some reason installing something with thru-bolts on area of core instead of a block out, you can acheive the same effect in holes as small as 1/4" by chucking an allen wrench into a cordless drill and using the right angled end to reef out the material as it spins. Requires practice. Sometimes it helps to use a bench grinder to make the allen wrench end the desired length for very small holes. I've seen people come up with all sorts of devices to acheive the same effect, but I have best results with router bits, which I happen to have a vast repertoire of at hand for different sizes. A drum sander can sometimes do the same job well but it's slow IMHO. Use tongue depressors for the cabosil fill, they work perfectly for a super smooth no sanding finish in cores up to 3/4". Above that you have to mix peanut butter thick and sometimes have to sand a little...

Balsa is a wonderful coring material if it is installed properly and the holes are always "double drilled". Any core material will deteriorate if it gets wet and is subject to freeze/thaw cycles. The people that installed the balsa core in the pictures did an awful job. Proper installation would inhibit water from migrating along the channels and would limit any deterioration to a very small area around the water entry point.

__________________Faithful are the Wounds of a Friend, but the Kisses of the Enemy are Deceitful! ........
A nation of sheep breeds a government of wolves!
Unprepared boaters, end up as floatsum!.......

Drill the size hole you want from the TOP.Do not drill through the bottom layer of glass.Chuck up a Aleen wrench thats about one inch bigger than your hole and insert.Enjoy the vibrations as it tears up the balsa core.Remove and shop vac all the torn up core out.Fill hole with a semi liquid epoxy.Re drill when epoxy is hard.No drips to the cabin and KISS.
Mark
Ps.If your doing a existing hole just remove the core with chucked up allen wrench and put a piece of duct tape on the bottom hole when epoxing.